Molecular crowding enhances facilitated diffusion of two human DNA glycosylases

Intracellular space is at a premium due to the high concentrations of biomolecules and is expected to have a fundamental effect on how large macromolecules move in the cell. Here, we report that crowded solutions promote intramolecular DNA translocation by two human DNA repair glycosylases. The crowding effect increases both the efficiency and average distance of DNA chain translocation by hindering escape of the enzymes to bulk solution. The increased contact time with the DNA chain provides for redundant damage patrolling within individual DNA chains at the expense of slowing the overall rate of damaged base removal from a population of molecules. The significant biological implication is that a crowded cellular environment could influence the mechanism of damage recognition as much as any property of the enzyme or DNA.A significant triumph in biochemistry over the last 20 years was the ability to isolate human DNA repair enzymes and study their in vitro properties using defined DNA substrates containing damaged sites. Typically, these studies have been performed using dilute conditions, where the concentration of the enzyme, DNA and buffer components were low compared to the concentration of water. Although a wealth of insights into the thermodynamic, kinetic and structural properties of enzymes have resulted from such approaches (1–7), DNA repair enzymes act in a crowded cellular environment with quite different physical properties (8,9). Thus, an open question is how the complex intracellular milieu affects the ability of enzymes to locate and repair damage sites embedded in a large polymeric DNA substrate.The human intracellular environment has numerous physical properties that could dramatically affect enzyme activity. These include high inorganic ion and metabolite concentrations (10,11), lower dielectric properties (12–14), higher bulk viscosity (15,16), and the presence of high concentrations of macromolecules which consume available volume (‘molecular crowding’) (17,18). Indeed, the concentration of macromolecules in human cells is an astounding ∼100–300 mg/ml (9,19), which means that 10–40% of the total cellular volume is consumed by large molecules (often called the excluded volume). Taken together,­ these parameters could affect association of an enzyme with its target in complex ways. For instance, high ion concentrations are expected to shield electrostatic interactions between an enzyme and its highly charged DNA substrate (10,20,21), while a lower dielectric constant could have an opposite effect. Increases in macroscopic viscosity will slow the translational movement of macromolecules and due to entropic effects, crowded environments will push macromolecular association when the complex consumes a smaller volume than the free component species (9,22,23).Although volume exclusion largely explains the effects of crowded environments on binding equilibria, crowding has been reported to have a surprisingly small effect on the diffusion-controlled association kinetics of macromolecules (24). Indeed, it has been observed that some diffusion-controlled association reactions occur at nearly the same rates in crowded solutions and in cells as they do in dilute solution (24,25). These kinetic effects are counterintuitive, but can be understood by considering that macromolecular crowders alter the macroscopic viscosity and available volume in crowded solutions, but do not change the microscopic viscosity (26,27). Thus, over short nanometer distances, the rotational and translational diffusion of proteins is not greatly affected by crowding because the protein only feels the microscopic viscosity of the solvent that is present in the spaces between the larger crowding molecules (28). Over larger distances, hard sphere repulsion between the protein and crowding molecules increases the effective viscosity and slows translational diffusion (8,28,29). When two binding partners approach one another, they are captured within a low viscosity (high mobility) cage created by the larger crowding molecules, which increases the probability for a productive encounter event. Surprisingly, the capture of two binding partners within a high mobility cage can in some cases offset all of the negative effects of high viscosity on the overall association rate (29).The above considerations raise the interesting question of what effect molecular crowding has on enzyme association with DNA, and in particular, the property of facilitated diffusion along a DNA chain? Facilitated diffusion on the DNA chain (‘translocation’) is a distinct process that involves transient states of an enzyme and DNA that are not directly observable in equilibrium binding, steady-state or rapid kinetic measurements (1–4,30). Here, we measure the effect of inert crowding agents on the probability that the DNA repair enzymes uracil and 8-oxguanine DNA repair glycosylase will successfully translocate between two damaged sites in a DNA chain. We find that crowding increases the likelihood that each enzyme will successfully translocate between their respective target sites without dissociation to bulk solution and also increases the average translocation distance. For both enzymes, crowding biases the damage search process toward a chain tracking search mode rather than a 3D search mode. Such a crowder-induced transition in the search mode could significantly impact the effectiveness of the damage search in a crowded nuclear environment. These enzymes represent two of the largest superfamilies of glycosylases and their similar behavior in these studies suggests that the findings will be general for other related glycosylases.     

Asymmetric reproductive character displacement in male aggregation behaviour

Reproductive character displacement--the evolution of traits that minimize reproductive interactions between species--can promote striking divergence in male signals or female mate preferences between populations that do and do not occur with heterospecifics. However, reproductive character displacement can affect other aspects of mating behaviour. Indeed, avoidance of heterospecific interactions might contribute to spatial (or temporal) aggregation of conspecifics. We examined this possibility in two species of hybridizing spadefoot toad (genus Spea). We found that in Spea bombifrons sympatric males were more likely than allopatric males to associate with calling males. Moreover, contrary to allopatric males, sympatric S. bombifrons males preferentially associated with conspecific male calls. By contrast, Spea multiplicata showed no differences between sympatry and allopatry in likelihood to associate with calling males. Further, sympatric and allopatric males did not differ in preference for conspecifics. However, allopatric S. multiplicata were more variable than sympatric males in their responses. Thus, in S. multiplicata, character displacement may have refined pre-existing aggregation behaviour. Our results suggest that heterospecific interactions can foster aggregative behaviour that might ultimately contribute to clustering of conspecifics. Such clustering can generate spatial or temporal segregation of reproductive activities among species and ultimately promote reproductive isolation.     

Advanced Intestinal Cancers often Maintain a Multi-Ancestral Architecture

A widely accepted paradigm in the field of cancer biology is that solid tumors are uni-ancestral being derived from a single founder and its descendants. However, data have been steadily accruing that indicate early tumors in mice and humans can have a multi-ancestral origin in which an initiated primogenitor facilitates the transformation of neighboring co-genitors. We developed a new mouse model that permits the determination of clonal architecture of intestinal tumors in vivo and ex vivo, have validated this model, and then used it to assess the clonal architecture of adenomas, intramucosal carcinomas, and invasive adenocarcinomas of the intestine. The percentage of multi-ancestral tumors did not significantly change as tumors progressed from adenomas with low-grade dysplasia [40/65 (62%)], to adenomas with high-grade dysplasia [21/37 (57%)], to intramucosal carcinomas [10/23 (43%]), to invasive adenocarcinomas [13/19 (68%)], indicating that the clone arising from the primogenitor continues to coexist with clones arising from co-genitors. Moreover, neoplastic cells from distinct clones within a multi-ancestral adenocarcinoma have even been observed to simultaneously invade into the underlying musculature [2/15 (13%)]. Thus, intratumoral heterogeneity arising early in tumor formation persists throughout tumorigenesis.     

Alpha-conotoxin residues that interact at close range with gamma-tyrosine-111 and mutant delta-tyrosine-113 on the Torpedo nicotinic acetylcholine receptor

The alpha-conotoxins MI and GI display stronger affinities for the alphagamma agonist site on the Torpedo californica electrocyte nicotinic acetylcholine receptor (ACHR) than for the alphadelta agonist site, while alpha-conotoxin SI binds with the same affinity to both sites. Prior studies reported that the arginine at position 9 on GI and the tyrosine at position 111 on the receptor gamma subunit were responsible for the stronger alphagamma affinities of GI and MI, respectively. This study was undertaken to determine if the alpha-conotoxin midchain cationic residues interact with Torpedo gammaY111. The findings show that lysine 10 on MI is responsible for the alphagamma selectivity of MI and confirm the previously reported importance of R9 on GI and on the SI analogue, SIP9R. The results also show that gammaY111 contributes substantially to the selective alphagamma high affinity of all three peptides. Double-mutant cycle analyses reveal that, in the alphagamma site, K10 on MI and R9 on SIP9R interact with the aromatic ring of gammaY111 to stabilize the high-affinity complex, while in contrast, R9 on GI does not. The substitution of Y for R at position 113 on the delta subunit converts the alphadelta site into a high-affinity site for MI, GI, and SIP9R through the interacting of deltaY113 with K10 on MI and with R9 on both GI and SIP9R. The overall data show that the residues in the two sites with which MI interacts, other than at gamma111/delta113, are either the same or similar enough to exert equivalent effects on MI, indicating that MI binds in the same orientation at the alphagamma and alphadelta sites. Similar findings show that SIP9R probably also binds in the same orientation at the wild-type alphagamma and alphadelta sites. The finding that R9 on GI interacts closely with deltaR113Y but not with gammaY111 means that GI binds in different orientations at the alphagamma and alphadelta sites. This report also discusses the molecular basis of the difference in the MI high-affinity sites on Torpedo and embryonic mouse muscle ACHRs.     

Intracellular trafficking of recycling apolipoprotein E in Chinese hamster ovary cells

We have investigated apolipoprotein E (apoE) recycling in Chinese hamster ovary (CHO) cells, a peripheral cell that does not produce lipoproteins or express apoE. Using a pulse-chase protocol in which cells were pulsed with 125I-apoE-VLDL and chased for different periods, approximately 30% of the apoE internalized during the pulse was resecreted within a 4 h chase in a relatively lipid-free state. The addition of lysosomotropic agents or brefeldin A had no effect on apoE recycling. Unlike previous results with hepatocytes and macrophages, neither apoA-I nor upregulation of ABCA1 stimulated apoE recycling. However, cyclodextrin, which extracts cholesterol from plasma membrane lipid rafts, increased recycling. Confocal studies revealed that apoE, internalized during a 1 h pulse, colocalizes with early endosomal antigen-1, Rab5, Rab11a, and lysobisphosphatidic acid but not with lysosomal-associated membrane protein-1. Colocalization of apoE and Rab11a persisted even after cells had been chased for 1 h, suggesting a pool of apoE within the endosomal recycling compartment (ERC). Our data suggest that apoE recycling in CHO cells is linked to cellular cholesterol removal via the ERC and phospholipid-containing acceptors in a pathway alternative to the ABCA1-apoA-I axis.     

The HtrA Protease from Streptococcus pneumoniae Digests Both Denatured Proteins and the Competence-stimulating Peptide

The HtrA protease of Streptococcus pneumoniae functions both in a general stress response role and as an error sensor that specifically represses genetic competence when the overall level of biosynthetic errors in cellular proteins is low. However, the mechanism through which HtrA inhibits development of competence has been unknown. We found that HtrA digested the pneumococcal competence-stimulating peptide (CSP) and constituted the primary extracytoplasmic CSP-degrading activity in cultures of S. pneumoniae. Mass spectrometry demonstrated that cleavage predominantly followed residue Phe-8 of the CSP-1 isoform of the peptide within its central hydrophobic patch, and in competition assays, both CSP-1 and CSP-2 interacted with HtrA with similar efficiencies. More generally, analysis of β-casein digestion and of digestion within HtrA itself revealed a preference for substrates with non-polar residues at the P1 site. Consistent with a specificity for exposed hydrophobic residues, competition from native BSA only weakly inhibited digestion of CSP, but denaturation converted BSA into a strong competitive inhibitor of such proteolysis. Together these findings support a model in which digestion of CSP by HtrA is reduced in the presence of other unfolded proteins that serve as alternative targets for degradation. Such competition may provide a mechanism by which HtrA functions in a quality control capacity to monitor the frequency of biosynthetic errors that result in protein misfolding.     

Defective Nodal and Cerl2 expression in the Arl13b(hnn) mutant node underlie its heterotaxia

Specification of the left-right axis during embryonic development is critical for the morphogenesis of asymmetric organs such as the heart, lungs, and stomach. The first known left-right asymmetry to occur in the mouse embryo is a leftward fluid flow in the node that is created by rotating cilia on the node surface. This flow is followed by asymmetric expression of Nodal and its inhibitor Cerl2 in the node. Defects in cilia and/or fluid flow in the node lead to defective Nodal and Cerl2 expression and therefore incorrect visceral organ situs. Here we show the cilia protein Arl13b is required for left right axis specification as its absence results in heterotaxia. We find the defect originates in the node where Cerl2 is not downregulated and asymmetric expression of Nodal is not maintained resulting in symmetric expression of both genes. Subsequently, Nodal expression is delayed in the lateral plate mesoderm (LPM). Symmetric Nodal and Cerl2 in the node could result from defects in either the generation and/ or the detection of Nodal flow, which would account for the subsequent defects in the LPM and organ positioning.